Les modifications de protéines, qu’elles soient post-traductionnelles (PTMs) ou induites chimiquement, ont une influence considérable sur l'activité des protéines. Des méthodes de spectrométrie de masse (MS) HRMS, MS/MS CID et ETD, et de biochimie ont été développées pour la caractérisation structurale et cinétique de complexes protéine-ligand et de PTMs, dans le but de disséquer leur mécanisme et de concevoir des médicaments covalents contre des protéines liant des protéases, des kinases, ou l'ADN. La MS combinée avec des outils biochimiques a permis de séquencer l'inhibiteur de protéases grégline, et de détecter une PTM originale. De même, la transposase MOS1, modèle de l'intégrase du VIH pour la conception d'inhibiteurs, s'avère être à la fois acétylée et phosphorylée. Pour la lyase Abf2, une stratégie de piégeage, purification, protéolyse et hydrolyse ADN du complexe covalent Abf2-ADN, couplée à l’analyse MS, a été développée. Enfin, l’interaction entre le surpresseur de métastase hPEBP1 et la locostatine a été disséquée sur la protéine entière et par approche bottom-up. La locostatine s’hydrolyse en butyrate après fixation. Afin d’identifier le site ciblé par la locostatine, les conditions de réaction et de protéolyse ont été optimisées. La présence de réactions non spécifiques a conduit au développement 1) d'un modèle mathématique permettant de déterminer la fraction de liaison optimale pour discriminer le site spécifique des sites non-spécifiques, et 2) d'une méthode pour la quantification parallèle et exhaustive du degré de modification de tous les sites modifiés d'une protéine. Ces outils sont applicables aux ligands covalents de protéines et/ou à leurs PTMs. / Protein modifications, whether post-translational (PTMs) or chemically induced, play a crucial role on the activity of proteins. Mass spectrometry (MS) techniques such as HRMS, CID/ETD MS/MS, and biochemistrybased methods for structural and kinetic characterization of protein-ligand complexes and PTMs have been developed. MS combined with several biochemical tools has been used to sequence the proteinase inhibitor gregline and to detect a novel PTM. A similar approach shows that the transposase MOS1, a model for the design of HIV integrase inhibitors, is both phosphorylated and acetylated. For the lyase Abf2, a strategy of trapping, purification, proteolysis, and DNA hydrolysis of the Abf2-DNA covalent complex, coupled to MS analysis, has been developed. Finally, the interaction between the metastasis suppressor hPEBP1 and locostatin was dissected. Upon binding to hPEBP1, locostatin undergoes hydrolysis. To identify the site targeted by locostatin, the conditions of reaction and proteolysis were optimized. The qualitative approach reveals the presence of non-specific reactions, leading to the development of 1) a mathematical model to determine the optimum bound fraction for discriminating the specific site from non-specific sites, and 2) a method for the parallel and exhaustive quantification of the degree of modification of all modified sites of a protein. These tools are widely applicable to covalent protein ligands and/or PTMs.

L'accès aux soins dentaires est devenu, au cours de ces dernières années, un service de plus en plus demandé par la population. En particulier, la pose d'un implant, destiné à remplacer une dent manquante, en recréant une racine artificielle, devient un acte de plus en plus courant. Une des principales sources de complications entrainant l'échec de la pose d'un implant est une maladie inflammatoire : la péri-implantite. Cette maladie induit la perte des os de soutien dans les tissus entourant l'implant fonctionnel. Actuellement, il n'existe pas d'implant prévenant ces infections bactériennes, seuls des traitements curatifs sont proposés. Le développement d'un traitement antibactérien implantaire apparaît alors comme une solution préventive pertinente pour limiter les complications post-opératoires et représente un défi de santé publique. Pour parvenir à cet objectif, dans ce travail de thèse, plusieurs solutions pour préparer un revêtement implantaire bioactif ont été étudiées et évaluées. Elles sont toutes basées sur le recouvrement d'une surface modèle de titane par un polymère naturel bioactif, le chitosane. Le greffage du biopolymère au substrat a été réalisé via une liaison covalente en utilisant un agent de couplage. Les différentes étapes de la synthèse du revêtement ainsi que ses propriétés biologiques ont été caractérisées à l'aide de techniques d'analyses de chimie de surface, par des études de tenue et de restitution du biopolymère en milieu acide ainsi que par des études in vitro de l'activité antibactérienne et des propriétés biologiques des revêtements. Les résultats de ce travail ont permis de sélectionner le revêtement bioactif possédant les meilleurs propriétés pour l'application visée, notamment en raison de sa tenue en milieu acide et de son activité antibactérienne en présence des bactéries communes / In the past years, population requirement for dental care service increased. More precisely, replacement of missing tooth using dental implant is now a common intervention. As implant provides an artificial root, this procedure is permanent. The failure of the placement procedure is mainly due to an inflammatory disease: peri-implantitis. This disease leads to the death of bone tissues surrounding the dental implant. Today only curative solutions are available, and no implants can prevent bacterial development. It appears that preventing post-surgical complications by designing antibacterial implants is now a public health issue. To achieve this goal, we evaluate in this thesis different solutions to design bioactive implant coatings. We focused our work on coating of a model titanium surface by a bioactive polymer: chitosan. Polymer binding on the substrate is achieved by covalent link using a coupling agent. We described each step of the coating synthesis and characterized its biological properties using both surface chemistry analysis and cell biology techniques. We studied its behavior in an acid environment and analyzed its biological and antibacterial properties in vitro. Results of this work were used to select the bioactive coating with the best properties for the intended application, particularly due to its resistance in acidic condition and its antibacterial activity against common bacteria

Silicone release liners are silicone coatings on top of papers or films that are used in the adhesives industry to prevent adhesion before the final use of the adhesive e.g. labels. The process of production of release liners involves the casting of molten polysiloxanes on top of the substrates that crosslink by hydrosilylation reaction forming silicone networks. The quality of the release liner can be assessed by diverse methods usually performed when the coating process has been finished. Rarely an online control of the reaction is possible. Fluorescence spectroscopy was found to be a non-invasive useful method to control the reaction during the whole process by introducing very small concentration of fluorescent molecules in the polymer formulations; those fluorophores are sensitive to environmental changes as the silicone polymer molecules crosslink. In response to that stimulus, the fluorescence intensity varies along the time upon reaction allowing the identification of the gel point and further modifications or molecules rearrangements in a post-curing stage within weeks that are non-observable with conventional quality control methods. It was found that the fluorescent molecules do not require to be attached covalently to the polysiloxanes, thus fluorescence spectroscopy is a simple method to implement for controlling the production of silicone coatings. Moreover, the characterization of several silicone formulations was performed to find the optimal conditions for the production of release liners and to understand the effect of every component in the formulation on the performance of the silicones. The kinetics of the reaction was also studied and even a mechanism for the hydrosilylation reaction was proposed.

[pt] No contexto da redução da concentração de CO2 na atmosfera e utilizar o mesmo na síntese de produtos de interesse, buscou-se sintetizar COFs com propriedades biomiméticas da enzima anidrase carbônica capaz de converter CO2. O chamado Tppa-NO2-COF foi planejado a partir dos blocos de construção triformilfluoroglucinol e 2-nitro 1,4-fenilenodiamina (comercialmente disponível). O triformilfluoroglucinol foi previamente sintetizado pela reação de Duff, entretanto outras metodologias alternativas foram testadas de forma a melhorar as condições reacionais e o custo atrelado ao processo. Em decorrência da não reprodutibilidade das metodologias sintéticas do Tppa-NO2-COF reportadas na literatura, foi necessário um processo de otimização (variando tipo e quantidade de solvente, concentração do ácido, condição reacional, entre outros). A influência do grupamento nitro no Tppa-NO2 foi igualmente avaliada, através da síntese do material análogo sem o nitro, o chamado Tppa-1-COF, o qual foi obtido com área de 434 m2/g, condizente com o dado reportado na literatura. Outra metodologia abordada para a síntese desses materiais foi a sonificação (sonochemistry) que demonstrou ser uma excelente alternativa para a síntese dos materiais de maneira eficaz e rápida. Entretanto, o material foi obtido com cristalinidade e área específica baixas e muito variáveis (de 40 a 628 m2/g), o que, por definição não pode ser chamado de COF, sendo então tratado como Covalent Organic Network (CON). Apesar da adversidade, seguiu-se com as modificações pós-sintéticas no Tppa-NO2-CON, realizando a redução do grupamento nitro e consequente reação do grupo amina para formar linkers que permitissem a atividade biomimética à enzima via ligação peptídica ou via triazol, capazes de se coordenar ao íon zinco. Otimizações ainda se fazem necessárias para a obtenção do COF, bem como estudos mais aprofundados nas modificações pós sintéticas e de adsorção de CO2, aplicação na conversão de CO2 a bicarbonato e outros produtos de interesse para a síntese orgânica. / [en] In the context of reducing the concentration of CO2 in the atmosphere and using it in the synthesis of products of interest, we sought to synthesize COFs with biomimetic properties of the carbonic anhydrase enzyme capable of converting CO2. The so-called Tppa-NO2-COF was designed from the building blocks triformylfluoroglucinol and 2-nitro 1,4-phenylenediamine (commercially available). Triformylfluoroglucinol was previously synthesized by the Duff reaction, however other alternative methodologies were tested in order to improve the reaction conditions and the cost linked to the process. Due to the non-reproducibility of synthetic methodologies of Tppa-NO2-COF reported in the literature, an optimization process (varying type and amount of solvent, acid concentration, reaction condition, among others) was necessary. The influence of the nitro group on Tppa-NO2 was also evaluated, through the synthesis of an analogous material without nitro, the so-called Tppa-1-COF, which was published with an area of 434 m2/g, consistent with what is reported in the literature. Another approach to synthetic materials for sonification (sonochemistry) includes being an excellent alternative for an efficient and rapid synthesis of materials. However, the material was found with low and highly variable crystallinity and specific area (from 40 to 628 m2/g), which, by definition, cannot be called COF, being treated as Covalent Organic Network (CON). Despite the adversity, post-synthetic modifications in the Tppa-NO2-CON followed, performing the reduction of the nitro group and consequent reaction of the amine group to form ligands that would allow a biomimetic activity to the enzyme via peptide bond or via triazole, from coordinate with the zinc ion. Optimizations are still necessary to obtain the COF, as well as in-depth studies on post-synthetic modifications and CO2 adsorption, application in the conversion of CO2 to bicarbonate and other products of interest to organic synthetic.

Les travaux présentés dans ce manuscrit portent sur la croissance de réseaux 2D covalents nanoporeux sur des substrats métalliques monocristallins en conditions ultravide. La réalisation de tels réseaux bidimensionnels nanostructurés met en jeu l’assemblage de briques élémentaires par des réactions de polymérisation sur surface qui sont ensuite caractérisées par microscopie à effet tunnel. La réaction étudiée est la condensation par déshydratation des groupes acides boroniques de l’acide 1,4-benzènediboronique conduisant à la formation d’un réseau aux pores hexagonaux de 15Å. L’étude se focalise spécifiquement sur l’influence de la fonctionnalisation du monomère (l’ajout de substituants ou d’hétéroatomes sur le cycle aromatique) sur les propriétés de la molécule et son impact sur la croissance du réseau. Une seconde famille de molécule fonctionnalisée a été étudié à partir de l’acide 1-bromo-4-benzèneboronique, qui par la substitution d’un acide boronique par un brome permet de modifier le mécanisme de polymérisation et ainsi de ralentir la cinétique de réaction. Les travaux réalisés portent sur la synthèse des deux familles de molécules, sur la caractérisation de l’évolution de leurs propriétés (polymérisation, dégradation) et sur leur capacité à former des réseaux covalents 2D ordonnés. Il a ainsi été possible de déterminer de manière qualitative les paramètres critiques qui gouvernent l’assemblage des molécules pour optimiser la croissance de réseaux fonctionnalisés. / The work presented in this thesis relates to the growth of 2D covalent organic frameworks on single crystal metal substrates in UHV conditions. The realization of such nanostructured two-dimensional networks involves the assembly of building blocks by polymerization reactions on surface that are characterised by scanning tunnelling microscopy. The chosen reaction is the condensation by dehydration of boronic acid groups from the 1,4-benzenediboronique acid leading to the formation of a nanoporous network with 15 Å hexagonal pores. The study focuses specifically on the effect of the monomer functionalization (addition of substituents or hetero atoms on the aromatic ring) regarding the molecule properties and its impact on the network growth. A second functionalized molecule family has also been studied from the 1-bromo-4-benzene boronic acid in which a boronic acid is substituted by a bromine group. This allows kinetic control of the polymerization. The work done relates to the synthesis of the two kind of functionalized molecules, the characterization of the evolution of their properties (polymerization, degradation) and their ability to form ordered 2D covalent networks. It was thus possible to determine qualitatively the critical parameters that govern the assembly of molecules to optimize the growth of functionalized networks.

In the past 30 years, the discovery of capabilities of nucleic acids far beyond their well-known information-bearing capacity has profoundly influenced our understanding of these polymers. The discovery by the Cech and Altman labs that nucleic acids could perform catalytic functions, coupled with the Gold and Szostak groups’ demonstration of the de novo evolution of nucleic acids that bind arbitrary ligands, has resulted in a proliferation of newfound roles for these molecules. Nucleic acids have found utility in both engineered systems, such as aptamer therapeutics, as well as in newly appreciated roles in extant organisms, such as riboswitches. As a result of these discoveries, many have pondered the potential importance of the dual (catalytic and informational) roles of nucleic acids in early evolution. A high-yielding synthetic route for the nonenzymatic polymerization of nucleic acids, based on the aqueous self-assembly of their components, would provide a powerful tool in nucleic acid chemistry, with potential utility in prebiotic and contemporary nucleic acid systems alike – however, such a route remains elusive. In this thesis, I describe several steps towards such a synthetic route. In these systems, a nucleic-acid binding ligand drives the assembly of short DNA and RNA duplexes, promoting the production of long nucleic acid polymers, while suppressing the production of short, cyclic species. Additionally, the use of a reversible covalent linkage allows for the production of long polymers, as well as the incorporation of previously cyclized products into these polymers. I also report several explorations of novel base pairings, nucleic acid-ligand interactions, and nucleic acid-ion interactions that have informed our studies of self-assembling nucleic acid systems.

Ce travail est consacré au développement d'une approche électrochimique permettant de préparer, à base de formes allotropiques différentes du carbone, divers matériaux poreux ayant comme : i) leurs éléments (feuillets de graphite, graphène, nanotubes et fullerène C60) sont attachés entre eux de façon covalente par les chaînes d'atomes du carbone de longueur différents, ii) les larges espaces internes (interstices ou les pores aléatoires) pouvant accommoder les cations, premièrement de métaux, plus grandes que Li+ (K+, Mg2+, mais aussi Alk4N+ etc.), iii) flexibilité tout en gardant la stabilité chimique des formes du carbone utilisées pour leur assemblage. Ainsi, une structure lamellaire à multicouches a été élaborée, une sorte du "graphite artificiel" avec les distances interstitielles à la demande : de 4.48 Å (avec -CH2- comme l'espaceur entre les couches) a 5.15 Å (avec -CH2C≡C-), contre 3.35 Å dans le graphite naturel. Élaborée dans ce travail, la méthode d'assemblage des matériaux stratifiés à base du graphite/graphène s'appuie sur le nouveau paradigme de greffage électrochimique aux interfaces carbonées (greffage électrophile, permettant de fixer à l'interface le linkeur CH2I ou CH2Br), et la fixation radicalaire d'une couche suivante par la réduction mono-électronique de sa liaison C-Hal. Les agents d'assemblage, Me3SiCH2I ou Me3SiC≡CCH2Br, dans un milieu universel CH3CN/0.1 M Bu4NPF6 ont été montrés être très efficaces pour ce processus. Un autre agent de couplage, 1,5-dibromopentane, a été utilisé pour assemblage cathodique (nucléophile/radicalaire) des nano-formes du carbone entre eux pour donner les matériaux poreux sans une structure spécifique régulière, les "nano-mousses", potentiellement convenable pour les anodes des batteries aux ions de Li et les batteries "post-Li-ions". Par la méthode combinée anodique/cathodique en utilisant Me3SiCH2I comme l'agent de fixation, un silsesquioxane F-@Ph8T8 avec l'ion fluorure encapsulé a été immobilisé sur le carbone vitreux ; l'interface ainsi préparée a montré son potentiel pour la détection d'exposition aux ions de Li+ ou de H+. Les structures préparées ont été étudiées par la voltampérométrie cyclique, chronocoulométrie, la spectroscopie d’impédance électrochimique et la spectroscopie électronique à balayage. / This work is dedicated to the development of an electrochemical approach to prepare, starting from different allotropic forms of carbon, various porous materials having particular features: i) their constituting elements (graphite sheets, graphene, nanotubes and fullerene C60) are covalently attached between them by the chains of carbon atoms of different length, ii) their large internal spaces (interstices or random pores) can accommodate the cations, - primarily metals, - larger than Li+ (e.g. K+, Mg2+, and also Alk4N+ etc.), iii) they are flexible while keeping the chemical stability of the carbon forms used for their assembly. Thus, a multilayered lamellar structure was developed, a kind of “artificial graphite” with interstitial distances on demand: from 4.48 Å (with -CH2- as the linker) to 5.15 Å (with -CH2C≡C-), against 3.35 Å in natural graphite. The method of assembly of graphite/graphene-based laminated materials developed in this work is based on the new electrochemical paradigm of grafting to carbon interfaces (electrophilic grafting, making possible to fix the CH2I or CH2Br functions at the interface) and the radical grafting of the subsequent layer by the mono electronic reduction of their C-Hal bond. New coupling agents, Me3SiCH2I or Me3SiC≡CCH2Br, in a universal CH3CN/0.1M Bu4NPF6 medium, have been shown to be very effective for this process. Another coupling agent, 1,5-dibromopentane, was used for cathodic (nucleophilic/radical) assembling of carbon nano forms between them to give porous materials without a regular specific structure, the “nano-sponges”, potentially suitable for making the anodes of Li-ion batteries and “post-Li-ion” batteries. Using the combined anodic/cathodic grafting method using Me3SiCH2I as the fixing agent, the fluoride encapsulating silsesquioxane F-@Ph8T8 was immobilized on glassy carbon; the thus prepared interface has shown its promise for devices detecting the exposure to Li+ or H+ ions. The prepared structures were studied by cyclic voltammetry, chronocoulometry, electro-chemical impedance spectroscopy and scanning electron spectroscopy.

[pt] Materiais bidimensionais apresentam possibilidades de funcionalização que os tornam versáteis para diversas aplicações, tais como em dispositivos eletrônicos. A presença de poros nesses materiais pode trazer novas funções, como adsorção de gases, liberação controlada de fármacos e catálise. Os covalent organic frameworks (COFs) são uma nova classe de materiais orgânicos porosos cristalinos que têm recebido destaque em química reticular. O objetivo dessa dissertação é apresentar a síntese e caracterização de quatro novos COFs baseados em carbazóis, que constitui uma classe de compostos utilizada na obtenção de polímeros condutores. O bloco de montagem principal utilizado foi o 3,6-diamino-9H-carbazol e as fontes de aldeído foram triformilfloroglucinol, triformilfenol, 1,3,5-tri(4-formilfenil)benzeno e triformilbenzeno para a síntese do RIO2, RIO3, RIO5 e RIO6, respectivamente. RIO2 e RIO3 apresentaram-se sob a forma ceto enamina e imina, respectivamente, além de pouca cristalinidade e baixa área específica. Através de cálculos baseados na Teoria do Funcional da Densidade (DFT), foi verificado que esses COFs apresentam suas folhas deslocadas e rotacionadas devido às interações eletrostáticas e para minimizar os momentos de dipolo das ligações N-H dos carbazóis. RIO5 e RIO6 também se apresentaram pouco cristalinos e com áreas específicas baixas. Apesar desses resultados, esses materiais ainda podem ser aplicados em eletrônica orgânica por apresentarem estrutura química compatível com tal aplicação. / [en] Two-dimensional materials have functionalization possibilities that make them versatile for various applications such as in electronic devices. The presence of pores in these materials can give new features to them, such as gas adsorption, drug delivery and catalysis. The covalent organic frameworks (COFs) are a new class of crystalline porous organic materials that have been prominent in reticular chemistry. The purpose of this work is to present the synthesis and characterization of four new COFs based on carbazoles, which are a class of compounds used to obtain conductive polymers. The main building block used was 3,6-diamine-9H-carbazole with the aldehyde sources were triformylphloroglucinol, triformylphenol, 1,3,5-tri(4 formylphenyl)benzene and triformylbenzene to obtain RIO2, RIO3, RIO5 and RIO6, respectively. RIO2 and RIO3 are in keto-enamine and imine form, respectively, as well as have low crystallinity and low specific area. Calculus based on Density Functional Theory (DFT) found that these COFs present their sheets displaced and rotated due to electrostatic interactions and to minimize the dipole moments of the N-H bonds of carbazoles. In an attempt to avoid the absence of pores, RIO5 and RIO6 materials were synthesized, however these COFs also performed poorly crystalline and with low specific areas. Despite these results, these materials can also be applied in organic electronics by presenting chemical structure compatible with such application.

This dissertation work focuses on the thermomechanical behaviors of two recent exciting developments in active polymers: shape memory (SM) effects and covalent adaptive network polymers with bond exchange reactions. Both polymers are active in performing prescribed functions when an external stimulus is applied. The goals of the studies are to understand complex thermomechanical behaviors of such smart polymers through experiments, develop constitutive models to describe the behaviors, and use the developed models to assist their development and engineering applications. For the polymer SM effect, we use a multi-branched constitutive model to study the SM effect achieved by polymer glass transition. The major finding of our study is that the “Reduced Time” is identified to be the unique parameter to determine the polymer shape fixity and recovery ratio under different thermo-temporal conditions in an SM cycle. Based on the theoretical knowledge, we also study the energy releasing mechanism within shape memory polymers (SMPs), multi-shape memory effects, as well as the SM properties in various composite systems, such as magnetic particles, carbon black and microvascular reinforced SMP composites. For the covalent adaptive network polymers, we adopt the emerging covalent chemistry BERs to achieve a malleable, reparable, recyclable and yet insoluble thermoset network. After being pulverized into micro-size, and then compressed either at high temperature or just facilitated by the moisture, the polymer powder could be welded on the interfaces, and assembled together into a new sample with comparable mechanical properties to the fresh sample. Theoretical models are developed to gain fundamental understanding of how the processing conditions can affect the quality of reprocessed materials. A molecular model is developed to understand welding kinetics at the interface. Such understanding is then used to develop a multiple length scale interfacial constitutive model, which can be implemented in to finite element simulation software to assist computational study of reprocessing process.

This dissertation presents efforts to expand the role of mass spectrometry (MS) in structural biology. Determination of quaternary structure of a protein complex has been hindered by limited fragmentation from collision-induced dissociation (CID). As an alternative, surface-induced dissociation (SID) was implemented for a quadrupole - time-of-flight instrument in the Wysocki laboratory. This research tested the hypothesis that SID should produce fragmentation reflective of subunit organization. Furthermore, ion mobility (IM) was used to prove the direct relationship between precursor conformation and observed dissociation patterns, and the relationship between activation and product ion conformation. The structure and dynamics of a dimeric small heat shock protein (sHSP) with no solved structure was investigated. The importance of N- and C-terminal domains for dimerization was determined, and the dimers were shown to exchange subunits. From exchange kinetics it is proposed that subunit exchange is unrelated to heat shock activity. SID was used to elucidate the subunit architecture of heterogeneous protein assemblies, including one previously solved protein structure and two formerly uncharacterized proteins. The heterohexamer toyocamycin nitrile hydratase dissociated into trimers, revealing the hexamer to be a dimer of trimers. The bacterial ribonuclease toxin:antitoxin tetramer was shown to have an antitoxin dimer at its core, with flanking individual toxin subunits. The examples presented here are the first clear proof that SID results can clearly indicate the substructure of a protein assembly.IM was used to study the conformation of precursor and product ions. A greater understanding of the relationship between precursor conformation and observed dissociation patterns was developed. Different charge states of a dodecameric sHSP were found to have significantly different conformations, which were directly reflected in SID spectra. IM comparison of CID and SID product ions showed that the same charge state of a product ion from either method has the same CCS. This suggests the product ion conformation is dependent upon ion charge state, and independent of activation method and collision energy. The cause and effect relationship between precursor conformation and MS/MS patterns, and activation and product ion conformation were clearly illustrated. Together, this body of research expands the role of MS for structural biology.